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Effect of VirR/VirS-VR-RNA regulatory cascade on the expression of chromosomal genes of Clostridium perfringens

ABSTRACT: The microarrays were subjected to two-color hybridization using Cy5 and Cy3 dyes incorporated in the cDNAs synthesized from total RNA samples of strains. We compared each gene’s transcription level between the wild-type (WT) strain 13 (labeled by Cy5) and the VirR-mutant strain (TS133) or VR-RNA-mutant strain (TS140) (both labeled by Cy3) on a single DNA microarray. Keywords: gene regulation in time course

ORGANISM(S): Clostridium perfringens str. 13

PROVIDER: GSE12833 | GEO | 2009/09/17

SECONDARY ACCESSION(S): PRJNA111143

REPOSITORIES: GEO

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Effect of VirR/VirS-VR-RNA regulatory cascade on the expression of chromosomal genes of Clostridium perfringens

Project description:The microarrays were subjected to two-color hybridization using Cy5 and Cy3 dyes incorporated in the cDNAs synthesized from total RNA samples of strains. We compared each geneâs transcription level between the wild-type (WT) strain 13 (labeled by Cy5) and the VirR-mutant strain (TS133) or VR-RNA-mutant strain (TS140) (both labeled by Cy3) on a single DNA microarray. Keywords: gene regulation in time course Each sample represent data calculated from 3 to 4 biological replicates of independent experiments. Each biological replicate contains duplicated data.

2010-05-05 | E-GEOD-12833 | biostudies-arrayexpress

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VirR and RevR regulate many Clostridium perfringens genes in a reciprocal manner

Project description:We further characterize the VirSR and RevR regulatory networks by profiling the C. perfringens strain JIR325 and its isogenic virR and revR regulatory mutants using strand-specific RNA-seq. Two independent biological replicates were sequenced for each strain, generating more than 90 million sequence reads for each RNA-seq library (wild type, 97,289,148 reads; virR mutant, 116,505,992 reads and revR mutant, 131,811,486 reads). Using the edgeR analysis package, 223 genes in the virR mutant and 88 genes in the revR mutant were found to be differentially expressed. Comparative transcriptomic analysis revealed that VirR acts as a global negative regulator, whilst RevR acts as a global positive regulator. Therefore, about 88% of the differentially expressed genes were up-regulated in the virR mutant, whereas 75% of the differentially expressed genes were down-regulated in the revR mutant. Importantly, we identified 22 genes that were regulated by both VirR and RevR. Of these genes, 18 or 82%, which included the sporulation-specific spoIVA, sigG and sigF genes, were regulated positively and negatively by RevR and VirR, respectively. Furthermore, mapped RNA-seq reads visualized as a user plot showed that there were 97 previously unannotated transcripts in the intergenic regions. These transcripts may potentially encode novel genes or small RNA molecules. This study has identified genes, antisense transcripts, and transcripts within intergenic regions and on the native plasmid, which are controlled by the VirSR or RevR regulatory system. The knowledge obtained will enable a more thorough annotation of the C. perfringens genome.

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Effect of virX regulator on the expression of chromosomal genes of Clostridium perfringens

Project description:The microarrays were subjected to two-color hybridization using Cy5 and Cy3 dyes incorporated in the cDNAs synthesized from total RNA samples of strains. We compared each geneM-bM-^@M-^Ys transcription level between the wild-type (WT) strain 13 (labeled by Cy5) and the virX-mutant strain (TS186) (labeled by Cy3) on a single DNA microarray. Total RNA was isolated from exponentially growing cells from thevirX mutant and the wild-type. Gene expression levels were compared between thevirX mutant and wild-type strain 13

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Project description:Effect of VirR/VirS-VR-RNA regulatory cascade on the expression of chromosomal genes of Clostridium perfringens

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